| 00_phyclust-package | Phyloclustering - Phylogenetic Clustering |
| 11_d.boundary.method | Boundary Methods for Population Proportions |
| 11_d.code.type | Code Types of Dataset and Substitution Models |
| 11_d.Color | Colors for Identifying Clusters in Plots |
| 11_d.edist.model | Evolution Distance Model |
| 11_d.EMC | EM Control |
| 11_d.EMControl | EM Control Generator |
| 11_d.em.method | EM Methods and Algorithms |
| 11_d.identifier | Identifiers for Evolution Models |
| 11_d.init.method | Initialization Methods for EM Algorithms |
| 11_d.init.procedure | Initialization Procedures for EM Algorithms |
| 11_d.label.method | Label Method |
| 11_d.se.model | Sequencing Error Model |
| 11_d.show.option | Show Available Options |
| 11_d.standard.code | Standard Codes and ids for Nucleotides, SNPs, Codon, Amino... |
| 11_d.substitution | Substitution Models for Mutation Processes |
| as.star.tree | Coerce a Rooted Tree to a Star Tree in Class phylo |
| bootstrap.seq | Bootstrap Sequences from a Fitted Model and Star Tree. |
| bootstrap.seq.data | Bootstrap a seq.data from a Fitted Model. |
| bootstrap.star.trees | Bootstrap a Star Tree from a Fitted Model. |
| bootstrap.star.trees.seq | Bootstrap Sequences from a Fitted Model. |
| code2nid | Transfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4) |
| code2snp | Transfer Nucleotide Codes / nids and SNPs / sids |
| data.fasta.pony | Great Pony 625 EIAV rev Dataset in the Fasta Format |
| data.phylip.crohn | Crohn's Disease SNP Dataset in the phylip Format |
| data.phylip.pony | Great Pony 524 EIAV rev Dataset in the phylip Format |
| file.read | Read Data from Files by Formats and Return a seq.data Object |
| file.write | Write Data to Files by Formats |
| find.best | Find the Best Solution of phyclust |
| find.consensus | Find the Consensus Sequence |
| gen.equal.star.anc.dec | Generate Comprehensive Trees. |
| gen.seq | Generate Sequences Given a Rooted Tree. |
| gen.star.tree | Generate a Rooted Tree with a Star Shape |
| gen.unit.K | Generate Comprehensive Trees. |
| getcut.fun | Tzeng's Method: Finding the Best Number of Clusters |
| get.rooted.tree.height | Get a Rooted Tree Height |
| haplo.post.prob | Tzeng's Method: Haplotype Grouping for SNP Sequences |
| ms | Generating Samples under a Wright-Fisher Neutral Model of... |
| nid.aid.cid | Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids... |
| paml.baseml | Phylogenetic Analysis by Maximum Likelihood for Nucleotide... |
| phyclust | The Main Function of phyclust |
| phyclust.edist | Evolution Distance of Sequences |
| phyclust.em.step | One EM-step of phyclust |
| phyclust.e.step | One E-Step of phyclust |
| phyclust.logL | Log-Likelihood of phyclust |
| phyclust.m.step | One M-Step of phyclust |
| phyclust.Pt | Transition Probabilities of phyclust Given Time |
| phyclust.se | The Main Function of phyclust for Sequencing Error Models |
| phyclust.se.update | Update phyclust Results by the Sequencing Error Model |
| phyclust.update | Update phyclust Results |
| plotdots | Dots Plots of Sequences for Visual Comparisons |
| plotgaps | Gaps Plots of Sequences for Visual Comparisons |
| plothist | Plot Histogram to Compare Number of Mutations. |
| plotnj | Plot an Unrooted Trees. |
| plotstruct | Struct Plots of Observations Based on Posterior Probabilities |
| print.summary | Functions for Printing or Summarizing Objects According to... |
| prune.Mu | Prune the Center Sequences Mu |
| read.seqgen | Read seqgen's Results and Return a seq.data |
| rescale.rooted.tree | Rescale a Rooted Tree's Height |
| RRand | Rand Index and Adjusted Rand Index |
| seq.data | A Toy Dataset in Class seq.data |
| seqgen | Seq-Gen |
| snp2sid | Transfer SNP codes (1, 2, -) and sids (0, 1, 2) |
| zz_all.internal | All Internal Functions of phyclust |
| zz_all.internal.tzeng | All Internal Functions of Tzeng's Methods |
